Also, Baptists in particular (and many evangelicals in general) like to remind us that the saints are all of us. We're all a bit scared of that whole "Saint" thing because that "smacks of Mariology, and Mary ain't a God!" (purposely mischaracterizing the doctrine, but sadly repeat sentiments I've heard...)
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Affable GeekMay 1 '12 at 18:25

@DoubtingThomas I'm not entirely certain the Catholic tradition of naming churches after saints and then completely forgetting why is much better. It's kind of nice that half of the Catholic churches in the USA seem to be St. Mary's, at least everyone knows who she is.
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Peter TurnerMay 1 '12 at 19:56

@PeterTurner plus with extra-biblical saints you have the added complication of disagreements about that person's character, etc. With a biblical concept or quote (or a biblical saint) at least everyone can agree that "grace" and "St. Mary" are biblical.
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Thomas ShieldsMay 1 '12 at 20:04

4 Answers
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As it happens, my local church is named after a saint who wasn't written up by name in the Bible. He was the founder of our church and his name was Emmanuel Peterson. (No prizes for correctly guessing whether the church uses his first or last name.)

I also found a non-denominational Protestant church called San Diego First Assembly. (That's probably cheating since the church was named after the city named after the saint.)

But as you noticed, naming churches after people (at least people not described in the Bible by name) is remarkably rare for Protestant denominations. The most likely reason is one you alluded to: Protestants have a different view of sainthood than the Orthodox or Catholic traditions. We have some reason not to put our trust in the names of people no matter who they were. As Luther said:

The more I read the books of the Fathers, the more I find myself offended; for they were but men, and, to speak the truth, with all their repute and authority, undervalued the books and writings of the sacred apostles of Christ.

Therefore, we Protestants are far more likely to name our churches after concepts, especially those found in the Bible. Alternatively, we use strictly descriptive names (cities mostly).

Concepts, usually, like the name of a city named after a saint. I'm piqued and amused by this defense, including dear Luther's, always. Tickled pink indeed. They don't really avoid it, I remember a church named 'Grandview' - what was Grandview? No idea. It was 'just a name' - would it not be better to name a church after someone who was at least good, rather than a place, which - what is it? But this is more an issue of Patronage, and Patronage is the reason for saint-naming.
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RiverCMay 2 '12 at 18:46

The answer depends on how you define "saint." If you use a protestant definition of the term, then any church named after a Christian (living or dead) is a church named after a saint. And there are many examples of this. A few I found quickly by google:

Round the corner from me there used to be a Methodist Church called St Aidan's. St Aidan was Bishop of Lindisfarne and died in 651. Potted biography.

So yes: it does happen. But I know of only that one.

[That particular church was closed some years ago due to structural problems and demolished. There's now a block of flats called St Aidan's Court on the site. I hope that wasn't the last Protestant church dedicated to a non-Biblical saint!]

Some Lutheran, Methodist, Presbyterian and Congregational churches are named after saints. The Reformed (Calvinistic) Churches, which theologically are very much the same as the Presbyterians (just historical differences, Presbyterianism born in the British Isles and Reformed Churches in the European Continent) very rarely have churches with name of saints, and I think (not sure) only in the United States. You can do that exercise: google "Saint (one very well known like Paul, or the evangelists) (succesively write Lutheran, Methodist, Presbyterian, Reformed) Church", and you will find lots of web sites of these churches. The Congregational churches are now part of the UNited Church of Christ so you must write "Saint (famous) United Church of Christ". Remember that denominations with British (Anglican, Methodist and Presbyterian) origins also have their patron saints (Saint George, Saint Andrew, Saint Patrick).